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Sample GSM1187595 Query DataSets for GSM1187595
Status Public on Jan 01, 2015
Title UC_inactive_1 [miRNA]
Sample type RNA
 
Source name colonic mucosal biopsy from UC patient with inactive disease
Organism Homo sapiens
Characteristics tissue: colon
disease: UC
disease activity: inactive
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the miRVAna miRNA isolation Kit (Ambion), according to the manufacturer's instructions. The integrity and quantity of total RNA and small RNA were assessed with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and a 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano kit and the Agilent Small RNA kit, respectively.
Label biotin
Label protocol Total RNA (250 ng) was used in a tailing reaction followed by ligation of the biotinylated signal molecule, using the FlashTag™ Biotin HSR RNA Labeling Kit (Genesphere) protocol for Affymetrix GeneChip miRNA arrays. As recommended, the labeling efficiency is verified with the ELOSA QC assay (Genesphere).
 
Hybridization protocol Incubation at 99°C for 5 minutes, followed by 45°C for another 5 minutes. Hybridization to GeneChip miRNA 2.0 arrays (Affymetrix) was performed under rotation (60 rpm) at 48°C for 16 hours. The arrays were washed and stained on an automated Fluidics Station (Affymetrix).
Scan protocol Microarrays were scanned on the Affymetrix 3000 GeneScanner. Intensity values for each probe cell (.cel file) were calculated using Affymetrix GeneChip Command Console (AGCC).
Description colonic mucosal microRNA expression data from UC patient with inactive disease
Data processing Quality control of the array data was performed with the Affymetrix miRNA QC Tool, version 1.1.1.0. Data were analyzed using RMA method in Bioconductor (R version 2.15.0).
 
Submission date Jul 17, 2013
Last update date Jan 01, 2015
Contact name Jan Van der Goten
E-mail(s) jan.vandergoten@med.kuleuven.be
Organization name KU Leuven
Department Clinical and Experimental Medicine
Lab TARGID - IBD Leuven
Street address Herestraat 49 bus 701
City Leuven
ZIP/Postal code 3000
Country Belgium
 
Platform ID GPL14613
Series (2)
GSE48957 Mucosal miRNA expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC)
GSE48959 Mucosal expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC)

Data table header descriptions
ID_REF
VALUE log2 values after RMA normalisation

Data table
ID_REF VALUE
1367452_st 0.74
1367453_st 0.70
1367454_st 0.99
1367455_st 0.79
1367456_st 1.16
1367457_st 0.79
1367458_st 1.02
1367459_st 0.60
1367460_st 0.86
1367461_st 0.87
1367462_st 0.64
1367463_st 1.22
1367464_st 0.58
1367465_st 0.81
1367466_st 0.97
1367467_st 0.98
1367468_st 0.97
1367469_st 0.95
1367470_st 0.62
1367471_st 0.86

Total number of rows: 20706

Table truncated, full table size 440 Kbytes.




Supplementary file Size Download File type/resource
GSM1187595_UC_inactive_1.CEL.gz 644.2 Kb (ftp)(http) CEL
Processed data included within Sample table

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